ArticleJournal of computational chemistry2018
Using the fast fourier transform in binding free energy calculations.
Article in Journal of computational chemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- High-throughput virtual screening of potential inhibitors of GPR52 using docking and biased sampling method for Huntington's disease therapy.Molecular diversity · 2024Article
- Article
- Docking-based long timescale simulation of cell-size protein systems at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model.Physical chemistry chemical physics : PCCP · 2022Article
- Unbinding ligands from SARS-CoV-2 Mpro via umbrella sampling simulations.Royal Society open science · 2022Article
- Implicit ligand theory for relative binding free energies: II. An estimator based on control variates.Journal of physics communications · 2020Article
- Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms.Journal of chemical theory and computation · 2020Article
- Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors.Journal of computational chemistry · 2020Article
- Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform.The journal of physical chemistry. B · 2019Article
- Alchemical Grid Dock (AlGDock) calculations in the D3R Grand Challenge 3 : Binding free energies between flexible ligands and rigid receptors.Journal of computer-aided molecular design · 2019Article
- Implicit ligand theory for relative binding free energies.The Journal of chemical physics · 2018Article
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3 authors.
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Abstract
According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the unbound ligand ensemble and a rigid receptor. Here, we use the fast Fourier transform (FFT) to efficiently evaluate BPMFs by calculating interaction energies when rigid ligand configurations from the unbound ensemble are discretely translated across rigid receptor conformations. Results for standard binding free energies between T4 lysozyme and 141 small organic molecules are in good agreement with previous alchemical calculations based on (1) a flexible complex ( R≈0.9 for 24 systems) and (2) flexible ligand with multiple rigid receptor configurations ( R≈0.8 for 141 systems). While the FFT is routinely used for molecular docking, to our knowledge this is the first time that the algorithm has been used for rigorous binding free energy calculations. © 2017 Wiley Periodicals, Inc.
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